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WO2008011565A3 - Method for identifying novel genes - Google Patents

Method for identifying novel genes Download PDF

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Publication number
WO2008011565A3
WO2008011565A3 PCT/US2007/073983 US2007073983W WO2008011565A3 WO 2008011565 A3 WO2008011565 A3 WO 2008011565A3 US 2007073983 W US2007073983 W US 2007073983W WO 2008011565 A3 WO2008011565 A3 WO 2008011565A3
Authority
WO
WIPO (PCT)
Prior art keywords
genes
novel
novel genes
homology
interest
Prior art date
Application number
PCT/US2007/073983
Other languages
French (fr)
Other versions
WO2008011565A2 (en
Inventor
Andre R Abad
Hua Dong
Susan B Lo
Billy F Mccutchen
Xiaomei Shi
Original Assignee
Pioneer Hi Bred Int
Du Pont
Andre R Abad
Hua Dong
Susan B Lo
Billy F Mccutchen
Xiaomei Shi
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority to DE602007004340T priority Critical patent/DE602007004340D1/en
Priority to AT07799738T priority patent/ATE455189T1/en
Priority to NZ574245A priority patent/NZ574245A/en
Priority to BRPI0715614-6A priority patent/BRPI0715614A2/en
Priority to AU2007275226A priority patent/AU2007275226B2/en
Priority to JP2009521018A priority patent/JP2009544288A/en
Application filed by Pioneer Hi Bred Int, Du Pont, Andre R Abad, Hua Dong, Susan B Lo, Billy F Mccutchen, Xiaomei Shi filed Critical Pioneer Hi Bred Int
Priority to EP07799738A priority patent/EP2046991B1/en
Priority to MX2009000775A priority patent/MX2009000775A/en
Priority to CA2658645A priority patent/CA2658645C/en
Publication of WO2008011565A2 publication Critical patent/WO2008011565A2/en
Publication of WO2008011565A3 publication Critical patent/WO2008011565A3/en
Priority to IL196624A priority patent/IL196624A0/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
    • C12N15/8279—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for biotic stress resistance, pathogen resistance, disease resistance
    • C12N15/8286—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for biotic stress resistance, pathogen resistance, disease resistance for insect resistance
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6851—Quantitative amplification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2527/00—Reactions demanding special reaction conditions
    • C12Q2527/107—Temperature of melting, i.e. Tm
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2531/00—Reactions of nucleic acids characterised by
    • C12Q2531/10—Reactions of nucleic acids characterised by the purpose being amplify/increase the copy number of target nucleic acid
    • C12Q2531/113—PCR
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2561/00—Nucleic acid detection characterised by assay method
    • C12Q2561/113—Real time assay
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12R—INDEXING SCHEME ASSOCIATED WITH SUBCLASSES C12C - C12Q, RELATING TO MICROORGANISMS
    • C12R2001/00—Microorganisms ; Processes using microorganisms
    • C12R2001/01—Bacteria or Actinomycetales ; using bacteria or Actinomycetales
    • C12R2001/07—Bacillus
    • C12R2001/075—Bacillus thuringiensis
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A40/00—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production
    • Y02A40/10—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production in agriculture
    • Y02A40/146—Genetically Modified [GMO] plants, e.g. transgenic plants

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  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Molecular Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biomedical Technology (AREA)
  • Microbiology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Plant Pathology (AREA)
  • Insects & Arthropods (AREA)
  • Pest Control & Pesticides (AREA)
  • Cell Biology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Peptides Or Proteins (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Agricultural Chemicals And Associated Chemicals (AREA)
  • Breeding Of Plants And Reproduction By Means Of Culturing (AREA)

Abstract

Methods and compositions for identifying novel genes that share regions of homology with known genes from target groups of genes of interest are provided. The methods comprise systematically designing oligonucleotide primers that are specific for regions of homology within the nucleotide sequences of a target group of known genes and performing successive rounds of PCR amplification of nucleic acid material from an organism of interest. The PCR steps are intended to identify and amplify nucleic acids comprising both known and novel genes. Nucleic acid molecules comprising known genes are detected and eliminated from further consideration by dot blot analysis using oligonucleotide probes specific for the known genes in the target group. Potentially novel genes are subjected to further sequence analysis to confirm novelty and assayed for biological activity. Compositions of the present invention include novel polynucleotides, and variants and fragments thereof, that comprise novel genes and the polypeptides encoded thereby.
PCT/US2007/073983 2006-07-21 2007-07-20 Method for identifying novel genes WO2008011565A2 (en)

Priority Applications (10)

Application Number Priority Date Filing Date Title
AT07799738T ATE455189T1 (en) 2006-07-21 2007-07-20 METHOD FOR IDENTIFYING NEW GENES
NZ574245A NZ574245A (en) 2006-07-21 2007-07-20 Method for identifying genes that are homologous to known pesticidal genes, particularly Bacillus thuringiensis (Bt) Cry genes
BRPI0715614-6A BRPI0715614A2 (en) 2006-07-21 2007-07-20 Methods for identifying new pesticide genes and new genes that show homology to a known target group of genes
AU2007275226A AU2007275226B2 (en) 2006-07-21 2007-07-20 Method for identifying novel genes
JP2009521018A JP2009544288A (en) 2006-07-21 2007-07-20 Methods for identifying new genes
DE602007004340T DE602007004340D1 (en) 2006-07-21 2007-07-20 METHOD OF IDENTIFYING NEW GENES
EP07799738A EP2046991B1 (en) 2006-07-21 2007-07-20 Method for identifying novel genes
MX2009000775A MX2009000775A (en) 2006-07-21 2007-07-20 Method for identifying novel genes.
CA2658645A CA2658645C (en) 2006-07-21 2007-07-20 Method for identifying novel genes
IL196624A IL196624A0 (en) 2006-07-21 2009-01-20 Method for identifying novel genes

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US83242306P 2006-07-21 2006-07-21
US60/832,423 2006-07-21

Publications (2)

Publication Number Publication Date
WO2008011565A2 WO2008011565A2 (en) 2008-01-24
WO2008011565A3 true WO2008011565A3 (en) 2008-05-02

Family

ID=38957650

Family Applications (3)

Application Number Title Priority Date Filing Date
PCT/US2007/073983 WO2008011565A2 (en) 2006-07-21 2007-07-20 Method for identifying novel genes
PCT/US2007/074006 WO2008011584A2 (en) 2006-07-21 2007-07-20 Bacillus thuringiensis toxin with anti-lepidopteran activity
PCT/US2007/074008 WO2008011586A2 (en) 2006-07-21 2007-07-20 Bacillus thuringiensis toxin with anti-coleopteran activity

Family Applications After (2)

Application Number Title Priority Date Filing Date
PCT/US2007/074006 WO2008011584A2 (en) 2006-07-21 2007-07-20 Bacillus thuringiensis toxin with anti-lepidopteran activity
PCT/US2007/074008 WO2008011586A2 (en) 2006-07-21 2007-07-20 Bacillus thuringiensis toxin with anti-coleopteran activity

Country Status (17)

Country Link
US (6) US7510878B2 (en)
EP (2) EP2044106A2 (en)
JP (1) JP2009544288A (en)
KR (1) KR20090054965A (en)
CN (3) CN101511864B (en)
AR (1) AR062020A1 (en)
AT (1) ATE455189T1 (en)
AU (1) AU2007275226B2 (en)
BR (1) BRPI0715614A2 (en)
CA (2) CA2658576C (en)
CL (1) CL2007002136A1 (en)
DE (1) DE602007004340D1 (en)
ES (1) ES2337952T3 (en)
IL (1) IL196624A0 (en)
MX (2) MX2009000774A (en)
NZ (1) NZ574245A (en)
WO (3) WO2008011565A2 (en)

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